The Modoc sucker (Catostomus microps) is a species that received legal protection in the United States based partially on concerns that anthropogenic environmental changes had restricted migration among populations and catalyzed hybridization with a congener, the Sacramento sucker (C. occidentalis). We applied eight microsatellite markers to samples of both species collected from throughout the range of Modoc suckers: two tributaries in the Pit River sub-basin and one tributary in the Goose Lake sub-basin. Modoc sucker populations in these three tributaries appeared to be largely isolated from one another: migration among Pit River tributaries appeared no greater than migration among sub-basins. Sacramento sucker populations appeared relatively more connected with one another, especially within the sub-basins. Interspecific hybrids were detected in all three tributaries. Tributaries in the Pit River sub-basin, which have retained typical habitats for both species, yielded relatively low proportions of hybrids (1.6% - 2.3%). The tributary in the Goose Lake sub-basin, which has undergone multiple cycles of hydrological change over the past two centuries, yielded a higher proportion of hybrids (10.9%). We conclude that hybridization between Modoc suckers and Sacramento suckers is not an active threat, but may be of conservation concern in situations where the habitat of one or both of these species has been eliminated or modified.